The investigators will develop and improve a DNA sequence assembly program for supporting large-scale DNA sequencing projects at public-funded genome centers. They developed a sequence assembly program named CAP3 in the initial project period. They propose to add new capabilities and make improvements to the CAP3 program. Specifically, the investigators will (1) improve the method for using forward-reverse constraints, (2) improve the method for generating consensus sequences, (3) add an option to support directed assembly in the sequence finishing phase, (4) add a capability to use databases of protein and EST sequences to order contigs produced in low-pass sequencing projects, and (5) add a capability to address alternative splicing patterns in assembly of EST sequences. They will work closely with Dr. Lee Hood's genome center. This relationship will ensure that their efforts on the assembly program will be relevant to real-world sequencing projects. The investigators will also assist the integration of their assembly program into sequencing environments at other genome centers.